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Yorodumi- PDB-7avj: Streptococcal High Identity Repeats in Tandem (SHIRT) domain 2 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7avj | ||||||
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Title | Streptococcal High Identity Repeats in Tandem (SHIRT) domain 2 from cell surface protein SGO_0707 | ||||||
Components | LPXTG cell wall surface protein | ||||||
Keywords | CELL ADHESION / Bacterial surface / adhesin / tandem repeat / Sgo0707 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus gordonii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.95 Å | ||||||
Authors | Whelan, F. / Jenkins, H.T. / Potts, J.R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Periscope Proteins are variable-length regulators of bacterial cell surface interactions. Authors: Whelan, F. / Lafita, A. / Gilburt, J. / Degut, C. / Griffiths, S.C. / Jenkins, H.T. / St John, A.N. / Paci, E. / Moir, J.W.B. / Plevin, M.J. / Baumann, C.G. / Bateman, A. / Potts, J.R. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Fragon: rapid high-resolution structure determination from ideal protein fragments. Authors: Jenkins, H.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7avj.cif.gz | 51.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7avj.ent.gz | 36.5 KB | Display | PDB format |
PDBx/mmJSON format | 7avj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/7avj ftp://data.pdbj.org/pub/pdb/validation_reports/av/7avj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9627.493 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus gordonii (strain Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288) (bacteria) Strain: Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288 Gene: SGO_0707 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8AW49 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.36 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7, 2.4 M Ammonium Sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.85 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2014 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.85 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→82.48 Å / Num. obs: 44546 / % possible obs: 95.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 8.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 0.95→0.96 Å / Mean I/σ(I) obs: 2.29 / Num. unique obs: 2604 / CC1/2: 0.839 / % possible all: 75.8 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 0.95→41.23 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.41 / SU ML: 0.01 / SU R Cruickshank DPI: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.49 Å2 / Biso mean: 15.717 Å2 / Biso min: 7.24 Å2
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Refinement step | Cycle: final / Resolution: 0.95→41.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.95→0.975 Å / Total num. of bins used: 20
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